Edits to 'https://fairsharing.org/FAIRsharing.2fbnkr' by 'Strambic' at 23:02, 12 Jul 2017 (approved):
'description' has been modified:
Before: The Minimum Information About Particle Tracking Experiments (MIAPTE) reporting guidelines is an OME-XML compatible metadata definition standard we hope will facilitate the sharing and dissemination of results obtained from Multiple Particle Tracking (MPT) experiments. Specifically, we hope that MIAPTE will contribute to make data produced in MPT experiments FAIR (Findable Accessible Interoperable and Reusable). For our purposes, MPT is defined as described by Chenouard et al. 2014. MIAPTE conforms to the criteria posited by Taylor et al. 2008 (https://doi.org/10.1038/nbt.1411) and currently maintained by the Minimum Information for Biological and Biomedical Investigations (MIBBI) foundry. MIAPTE can also be seen as an extension of the OME-XML data model in that elements, attributes and types defined in that model are re-used here when appropriate to avoid "reinventing the wheel". The current version of the model should be intended as a Request for Comments type of publication. Any member of the scientific or developer community is invited to collaborate with us to help us to modify|extend|improve the model.
After: The proposed Minimum Information About Particle Tracking Experiments (MIAPTE) reporting guidelines described here aims to deliver a set of rules representing the minimal information required to report and support interpretation and assessment of data arising from intracellular multiple particle tracking (MPT) experiments. Examples of such experiments are those tracking viral particles as they move from the site of entry to the site of replication within an infected cell, or those following vesicular dynamics during secretion, endocytosis, or exocytosis. By promoting development of community standards, MIAPTE will contribute to making MPT data FAIR (Findable Accessible Interoperable and Reusable). Ultimately, the goal of MIAPTE is to promote and maximize data access, discovery, preservation, re-use, and re-purposing through efficient annotation, and ultimately to enable reproducibility of particle tracking experiments. The MIAPTE guidelines are intended for different categories of users: 1) Scientists with the desire to make new results available in a way that can be interpreted unequivocally by both humans and machines. For this class of users, MIAPTE provides data descriptors to define data entry terms and the analysis workflow in a unified manner. 2) Scientists wishing to evaluate, replicate and re-analyze results published by others. For this class of users MIAPTE provides descriptors that define the analysis procedures in a manner that facilitates its reproduction. 3) Developers who want to take advantage of the schema of MIAPTE to produce MIAPTE compatible tools. MIAPTE consists of a list of controlled vocabulary (CV) terms that describe elements and properties for the minimal description of particle tracking experiments, with a focus on viral and vesicular traffic within cells. As part of this submission we provide entity relationship (ER) diagrams that show the relationship between terms. Finally, we also provide documents containing the MIAPTE-compliant XML schema describing the data model used by Open Microscopy Environment inteGrated Analysis (OMEGA), our novel particle tracking data analysis and management tool, which is reported in a separate manuscript. MIAPTE is structured in two sub-sections: 1) Section 1 contains elements, attributes and data structures describing the results of particle tracking, namely: particles, links, segments and trajectories. 2) Section 2 contains details about the algorithmic procedure utilized to produce and analyze trajectories as well as the results of trajectory analysis. In addition MIAPTE includes those OME-XML elements that are required to capture the acquisition parameters and the structure of images to be subjected to particle tracking The current version of the model|MIAPTE v02| is intended to be a Request for Comments (Crocker and Postel|2008). Members of the scientific and developer communities are invited to collaborate with us to modify|extend|and improve the model.
Edits to 'https://fairsharing.org/FAIRsharing.2fbnkr' by 'Strambic' at 03:16, 02 Jun 2017 (approved):
'description' has been modified:
Before: The Minimum Information About Particle Tracking Experiments (MIAPTE) reporting guidelines is an OME-XML compatible metadata definition standard we hope will facilitate the sharing and dissemination of results obtained from Multiple Particle Tracking (MPT) experiments. Specifically, we hope that MIAPTE will contribute to make data produced in MPT experiments FAIR (Findable Accessible Interoperable and Reusable). For our purposes, MPT is defined as described by Chenouard et al. 2014. MIAPTE conforms to the criteria posited by Taylor et al. 2008 and currently maintained by the Minimum Information for Biological and Biomedical Investigations (MIBBI) foundry. MIAPTE can also be seen as an extension of the OME-XML data model in that elements, attributes and types defined in that model are re-used here when appropriate to avoid "reinventing the wheel". The current version of the model should be intended as a Request for Comments type of publication. Any member of the scientific or developer community is invited to collaborate with us to help us to modify|extend|improve the model.
After: The Minimum Information About Particle Tracking Experiments (MIAPTE) reporting guidelines is an OME-XML compatible metadata definition standard we hope will facilitate the sharing and dissemination of results obtained from Multiple Particle Tracking (MPT) experiments. Specifically, we hope that MIAPTE will contribute to make data produced in MPT experiments FAIR (Findable Accessible Interoperable and Reusable). For our purposes, MPT is defined as described by Chenouard et al. 2014. MIAPTE conforms to the criteria posited by Taylor et al. 2008 (https://doi.org/10.1038/nbt.1411) and currently maintained by the Minimum Information for Biological and Biomedical Investigations (MIBBI) foundry. MIAPTE can also be seen as an extension of the OME-XML data model in that elements, attributes and types defined in that model are re-used here when appropriate to avoid "reinventing the wheel". The current version of the model should be intended as a Request for Comments type of publication. Any member of the scientific or developer community is invited to collaborate with us to help us to modify|extend|improve the model. Organisations have changed: Previous values: University of Massachusetts Medical School|USA Program in Molecular Medicine|University of Massachusetts Medical School SystemsX.ch New values: Program in Molecular Medicine|University of Massachusetts Medical School SystemsX.ch University of Massachusetts Medical School|USA Support links have changed: Previous values: http://big.umassmed.edu/omegaweb/miapte/miapte-2/miapte-section-1-elements-describing-particles-links-segments-and-trajectories/ http://big.umassmed.edu/omegaweb/miapte/miapte-2/miapte-section2-elements-describing-tracking-and-motion-analysis-procedures/ http://big.umassmed.edu/omegaweb/miapte/miapte-2/ New values: https://goo.gl/vdfTJx https://goo.gl/tjZjfl http://big.umassmed.edu/omegaweb/miapte/miapte-2/
Edits to 'https://fairsharing.org/FAIRsharing.2fbnkr' by 'Strambic' at 03:05, 02 Jun 2017 (approved):
'description' has been modified:
Before: The Minimum Information About Particle Tracking Experiments (MIAPTE) data model is an OME-XML compatible metadata definition standard we hope will facilitate the sharing and dissemination of results obtained from Multiple Particle Tracking (MPT) experiments. For our purposes, MPT is defined as described by Chenouard et al. 2014. MIAPTE conforms to the criteria posited by Taylor et al. 2008 and currently maintained by the Minimum Information for Biological and Biomedical Investigations (MIBBI) foundry. MIAPTE can also be seen as an extension of the OME-XML data model in that elements, attributes and types defined in that model are re-used here when appropriate to avoid "reinventing the wheel". The current version of the model should be intended as a Request for Comments type of publication. Any member of the scientific or developer community is invited to collaborate with us to help us to modify|extend|improve the model.
After: The Minimum Information About Particle Tracking Experiments (MIAPTE) reporting guidelines is an OME-XML compatible metadata definition standard we hope will facilitate the sharing and dissemination of results obtained from Multiple Particle Tracking (MPT) experiments. Specifically, we hope that MIAPTE will contribute to make data produced in MPT experiments FAIR (Findable Accessible Interoperable and Reusable). For our purposes, MPT is defined as described by Chenouard et al. 2014. MIAPTE conforms to the criteria posited by Taylor et al. 2008 and currently maintained by the Minimum Information for Biological and Biomedical Investigations (MIBBI) foundry. MIAPTE can also be seen as an extension of the OME-XML data model in that elements, attributes and types defined in that model are re-used here when appropriate to avoid "reinventing the wheel". The current version of the model should be intended as a Request for Comments type of publication. Any member of the scientific or developer community is invited to collaborate with us to help us to modify|extend|improve the model. Organisations have changed: Previous values: University of Massachusetts Medical School|USA SystemsX.ch Program in Molecular Medicine|University of Massachusetts Medical School New values: SystemsX.ch Program in Molecular Medicine|University of Massachusetts Medical School University of Massachusetts Medical School|USA
Edits to 'https://fairsharing.org/FAIRsharing.2fbnkr' by 'Strambic' at 03:31, 08 Oct 2016 (approved):
'description' has been modified:
Before: The Minimum Information About Particle Tracking Experiments (MIAPTE) data model is an OME-XML compatible metadata definition standard for capturing particle tracking, motion analysis results and analysis definition parameters in experimental biology.
After: The Minimum Information About Particle Tracking Experiments (MIAPTE) data model is an OME-XML compatible metadata definition standard we hope will facilitate the sharing and dissemination of results obtained from Multiple Particle Tracking (MPT) experiments. For our purposes, MPT is defined as described by Chenouard et al. 2014. MIAPTE conforms to the criteria posited by Taylor et al. 2008 and currently maintained by the Minimum Information for Biological and Biomedical Investigations (MIBBI) foundry. MIAPTE can also be seen as an extension of the OME-XML data model in that elements, attributes and types defined in that model are re-used here when appropriate to avoid "reinventing the wheel". The current version of the model should be intended as a Request for Comments type of publication. Any member of the scientific or developer community is invited to collaborate with us to help us to modify|extend|improve the model. Support links have changed: Previous values: New values: http://big.umassmed.edu/omegaweb/miapte/miapte-2/miapte-section-1-elements-describing-particles-links-segments-and-trajectories/ http://big.umassmed.edu/omegaweb/miapte/miapte-2/ http://big.umassmed.edu/omegaweb/miapte/miapte-2/miapte-section2-elements-describing-tracking-and-motion-analysis-procedures/
Minimum Information About Particle Tracking Experiments
